.TH genconf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
genconf - multiplies a conformation in 'random' orientations

.B VERSION 4.5
.SH SYNOPSIS
\f3genconf\fP
.BI "\-f" " conf.gro "
.BI "\-o" " out.gro "
.BI "\-trj" " traj.xtc "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-nbox" " vector "
.BI "\-dist" " vector "
.BI "\-seed" " int "
.BI "\-[no]rot" ""
.BI "\-[no]shuffle" ""
.BI "\-[no]sort" ""
.BI "\-block" " int "
.BI "\-nmolat" " int "
.BI "\-maxrot" " vector "
.BI "\-[no]renumber" ""
.SH DESCRIPTION
\&genconf multiplies a given coordinate file by simply stacking them
\&on top of each other, like a small child playing with wooden blocks.
\&The program makes a grid of \fI user defined\fR
\&proportions (\fB \-nbox\fR), 
\&and interspaces the grid point with an extra space \fB \-dist\fR.


\&When option \fB \-rot\fR is used the program does not check for overlap
\&between molecules on grid points. It is recommended to make the box in
\&the input file at least as big as the coordinates + 
\&Van der Waals radius.


\&If the optional trajectory file is given, conformations are not
\&generated, but read from this file and translated appropriately to
\&build the grid.
.SH FILES
.BI "\-f" " conf.gro" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

.BI "\-o" " out.gro" 
.B Output
 Structure file: gro g96 pdb etc. 

.BI "\-trj" " traj.xtc" 
.B Input, Opt.
 Trajectory: xtc trr trj gro g96 pdb cpt 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-nbox"  " vector" " 1 1 1" 
 Number of boxes

.BI "\-dist"  " vector" " 0 0 0" 
 Distance between boxes

.BI "\-seed"  " int" " 0" 
 Random generator seed, if 0 generated from the time

.BI "\-[no]rot"  "no    "
 Randomly rotate conformations

.BI "\-[no]shuffle"  "no    "
 Random shuffling of molecules

.BI "\-[no]sort"  "no    "
 Sort molecules on X coord

.BI "\-block"  " int" " 1" 
 Divide the box in blocks on this number of cpus

.BI "\-nmolat"  " int" " 3" 
 Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system!

.BI "\-maxrot"  " vector" " 180 180 180" 
 Maximum random rotation

.BI "\-[no]renumber"  "yes   "
 Renumber residues

.SH KNOWN PROBLEMS
\- The program should allow for random displacement of lattice points.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
